IMO they're too different to compare, I have never seen evidence of ego or prima donna's in San Antonio, just good hardworking team players who all know their roles and stay within the confines of a proven, (albeit boring) system, that teaches fundamental defense and teamwork. Credit the excellent front office for signing suchlike players and knowing what players will work within the system, credit Pop for meshing them like a well oiled machine. That said, Greg Popavich would have been an ABSOLUTE DISASTER coaching a team like the Shaq/Kobe Lakers, with all the ego's, drama, and divergent personalities, the players unwilling or unable to work within a proven system would have overwhelmed someone like him. Pop needs players that are essentially yes men, and that's OK, their great success proves there is nothing wrong with that, and they seem to enjoy playing together. Phil would have been successful there, but not like Pop, his style is too hands off, too mental, and the only real thinkers that I can see out there for SA is Manu and to a lesser extent Parker, great at creativity and adapting to a given situation, Duncan is the pentultimate post player waiting for the play to develop around him. Not a knock on him either, he's the best in the world at what he does.
The Jordan led Bulls were perfect for Phil's style because not only did he not have to get to involved in the game time fit and finish of the individual players and their roles within the scope of the game, he didn't even have to interact in the locker room. The reason? Michael Jordan was in ABSOLUTE AND TOTAL CONTROL of those players and they all knew it. Even though his ego was bigger than Shaq and Kobe's combined, he commanded respect and submission like no other player before or since. Consequently, if Phil said this is the way it will be, and because Jordan totally bought into that system, (and rightly so) it was Jordan who made sure everyone cooperated or else. Can you imagine Pippen disrespecting Phil like he did in the series against Indiana if Jordan was still in the lineup? Not hardly, Jordan's absense allowed ego's other than his own to assert themselves. Phil ran into a completely different animal in LA, Shaq and Kobe's massive ego's, the lack of respect they had for each other, the lack of respect they commanded or earned from their teammates, the disfunction that is LA, all combined to show us how good Phil is at one thing, managing ego's, and he did it in ways we never saw in Chicago, despite his reputation for exactly that. I do not believe ANYONE, not even my favorite coach of all time, Pat Riley, could have coaxed 3 championships out of that crazy group like Phil Jackson did. Phil is a master of surrounding himself with talent, both on the floor and in the coaching staff, we all know Tex Winter is primarily responsible for the X's and O's success of Phil's teams. Pop is good at X's, O's, and good old hard work.
So while Pop is IMO a great coach, Phil is a great manager, far too different in style to be compared.